Genotyping BC1_LD Pigs with SNP Arrays

A total of 197 animals from the BC1_LD (160 backcrossed individuals and their respective parents) were genotyped with the Porcine SNP60 Beadchip (Illumina), following the Infinium HD Assay Ultra protocol (Illumina)56 (link). Raw data were visualized with GenomeStudio software (Illumina) and trimmed for high genotyping quality (call rate >0.99). Markers with minor allele frequency (MAF) >5% and animals with missing genotypes <5% were retained. After the quality control filter, a subset of 40,586 SNPs and 197 animals remained.
Furthermore, the BC1_LD animals were genotyped with two SNPs within the ACSM5 (rs331702081) and IGF2 (IGF2-intron3-G3072A) genes using Taqman OpenArray^TM genotyping plates custom-designed in a QuantStudio^TM 12K flex Real-Time PCR System (ThermoFisher Scientific) (Supplementary Table S7) and the pyrosequencing protocol previously described27 (link), respectively.

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Puig-Oliveras A., Revilla M., Castelló A., Fernández A.I., Folch J.M, & Ballester M. (2016). Expression-based GWAS identifies variants, gene interactions and key regulators affecting intramuscular fatty acid content and composition in porcine meat. Scientific Reports, 6, 31803.

Publication 2016

Porcine SNP60 Beadchip Infinium HD Assay Ultra GenomeStudio software QuantStudioTM 12K flex Real-Time PCR System

Animals Assay Genes Igf2 Parents Porcine Snps

Corresponding Organization :

Other organizations : Universitat Autònoma de Barcelona, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Center for Research in Agricultural Genomics

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